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. 2019 Dec 11;9:18785. doi: 10.1038/s41598-019-55266-9

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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(a) Two modelled frontal-binding MMP-3:III-40d complexes shown as ribbons in the standard MMP-3 orientation. MMP-3 chain, white; Zn²⁺, magenta. THP chains: leading, blue; middle, green; trailing, red. Circles, close-up views of MMP-3:III-40d hydrogen bond networks (black lines), with the bonding residues represented as sticks coloured by heteroatom: N, navy blue; O, red, and labelled with 1-letter codes. (b) Close-up view of the modelled MMP-3:III-40d interfaces. The THP is represented as in (a), with side chains containing at least one atom located within 4 Å of the MMP-3 shown as sticks coloured by heteroatom: N, navy blue; O, red. MMP-3 is shown as solvent-accessible surface (UCSF Chimera⁷⁵) coloured according to the interfacing THP chains (4 Å distance). IDs of the staggered residues in the III-40d THP are roughly indicated (dashed lines). The P1’ and P10’ sites (nomenclature³⁷) are indicated for complex 2. In each complex, all three chains of the THP make contacts with MMP-3. (c) Theoretical analysis of the effects of III-40d residue substitutions on MMP-3 binding. MMP-3 is shown as white and transparent SAS and III-40d is shown as in (a), with modelled Arg side chains and hydrogen-bonded MMP-3 residues represented with sticks coloured by heteroatom: N, navy blue; O, red. Arg at the position Y of the Triplets −1 and 0 causes severe clashes with MMP-3 only in complex 2. (d) Top, NACCESS³⁶ computation of the modelled MMP-3:III-40d interface areas, colour-coded as in (b). Pie charts indicate the polar and nonpolar fractions of the total interface area for each modelled complex. Bottom, PDBePISA computation of the MMP-3:III-40d binding energies in each modelled complex. ΔG^int, estimated solvation free energy gain upon complex formation, excluding the effect of satisfied hydrogen bonds and salt bridges across the interfaces. ΔG^int < 0 corresponds to hydrophobic interfaces, or positive protein affinity. The ΔG^int P-value indicates interface specificity: P = 0.5, not specific; P > 0.5, likely an artefact; P < 0.5, likely interaction-specific. ΔG^diss, estimated free energy needed to dissociate the assembly; interfaces with ΔG^diss > 0 are thermodynamically stable.